DNA. ncrna. Non-coding RNA analysis for gene expression regulation using bioinformatics tools

Transcription

1 non-coding RNA DNA RNA RNA non-coding RNA ncrna ncrna ncrna ncrna ncrna ncrna ncrna ncrna ncrna non-coding RNA Non-coding RNA analysis for gene expression regulation using bioinformatics tools Hayashi Chisato 1 Kwon Yeondae 2 Miyazaki Satoru 2 Abstract: Advances in genome analysis have revealed that a genomic DNA contains gene coding regions other than protein coding sequences and transcription-regulating regions. Among these regions, there exist RNA coding regions involved in transcription regulation as a primary function, RNAs transcribed from these regions are referred to as non-coding RNAs (ncrnas). ncrnas are known to affect regulation of transcription, but many functions are still unknown. On the other hand, since some ncrnas specifically express in a particular disease, they may have potential for being used as drug targets. Also, while most of ncrnas currently observed locate on intergenic regions of protein coding genes, some ncrnas locate on intronic regions of protein coding genes. The aim of this work is to predict ncrnas as drug targets regulating disease-associated genes based on positional relationship between protein genes and ncrnas on a genome. In this paper, we compare ncrnas located on intronic regions across species. Keywords: non-coding RNA, gene expression, intron, database 1. 1 Graduate School of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba , Japan 2 Department of Medical and Life Science, Faculty of Pharmaceutical Sciences, Tokyo University of Science DNA RNA DNA c 2013 Information Processing Society of Japan 1

2 [1] RNA non-coding RNA ncrna ncrna [2], [3] ncrna ncrna small ncrna 200 ncrna long ncrna ncrna small ncrna RNA RNA interference: RNAi [4] RNAi ncrna mirna mrna [5] mirna [6], [7] mirna RNAi small ncrna long ncrna small ncrna long ncrna [8] long ncrna long ncrna [9], [10], [11] ncrna ncrna ncrna ncrna 2. ncrna mrna RNA snorna mrna snorna [12] ncrna [13] ncrna ncrna 1 2 ncrna Gene 3. intronic ncrna ncrna ncrna ncrna ncrna ncrna ncrna 3.1 ncrna ncrna H. sapiensm. musculusr. norvegicusd. melanogasters. cerevisiae C. elegans 6 Ensembl Genome [14] http: //asia.ensembl.orgindex.html ncrna Gene sets ncrna Transcript Sequence ncrna c 2013 Information Processing Society of Japan 2

3 1 ncrna intronic ncrna Organism ncrna intergenic intronic sense ncrna ncrna ncrna % H. sapiens 19,505 15,962 2, M.musculus 7,886 6,418 1, R. norvegicus 4,828 3, D. melanogaster 1,396 1, C. elegans 23,872 20,116 3, S. serevisiae intronic ncrna STATUS STSTUS H.sapiens M.musculus R.norvegicus D.melanogaster C.elegans S.cerevisiae mirna sense intronic sense over-lapping 13 2 misc RNA lincrna non coding/ncrna rrna snorna snrna trna prime over-lapping ncrna 18 2 ncrna host 2 pseudogene 415 Transcript locationncrna ncrna Gene 3 1 Gene Protein location Protein status ncrna Ensembl Gene sets protein coding ncrna ncrna 3 3 n 5 5 ( 1 ) intergenic ncrna ncrna n ncrna ncrna n+1 ( 2 ) intronic ncrna ncrna n ncrna ncrna 3 ncrna n+1 ( 3 ) sense ncrna ncrna ncrna ncrna 1 ncrna ncrna intronic ncrna 3.3 intronic ncrna STATUS 2 1 intronic ncrna STATUS 3.4 intronic ncrna intronic ncrna 2 ncrna RNAi mirna [5] intronic ncrna X c 2013 Information Processing Society of Japan 3

4 4 X mirna ENST ENSMUST 1 ncrna X intronic ncrna mirna ClustalX [15] 75 4 [16] 5 21 bl2seq [17] ncrna 1 ncrna RNAi ncrna intronic ncrna 2 ncrna mirna ncrna ncrna 4.2 intronic ncrna % ENST ENSMUST ENST ENST ENST ENSMUST ENST ENSMUST ENST ENST ENSMUST ENSMUST ENST ENST ENST ENST ENSMUST ENST ENSMUST ENSMUST ENST ENST ENST ENST ENSMUST ENST ENSMUST ENST ENST ENST ENST ENSMUST ENSMUST ENST ENSMUST ENST ENSMUST ENSMUST ENSMUST ENSMUST ENST ENST ENST ENSMUST ENST ENSMUST ENST ENSMUST ENST ENSMUST ENST ENST ENSMUST ENST ENSMUST ENSMUST ENSMUST ENSMUST ENST ENSMUST ENST ENSMUST ENSMUST ENST ENSMUST ENSMUST ENSMUST ENSMUST ENSMUST ENST ENSMUST ENST ENSMUST ENST ENSMUST X intronic mirna (Mean SD) 3 ncrna 5 mirna mirna node ncrna c 2013 Information Processing Society of Japan 4

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